This class implements generic methods for sequences with residue-basedmeta information. Meta sequences with meta data are Bio::LocatableSeqobjects with additional methods to store that meta information. SeeBio::LocatableSeq and Bio::Seq::MetaI.The meta information in this class is always one character per residuelong and blank values are space characters (ASCII 32).After the latest rewrite, the meta information no longer covers allthe residues automatically. Methods to check the length of metainformation (meta_length)and to see if the ends are flushed to thesequence have been added (is_flush). To force the oldfunctionality, set force_flush to true.It is assumed that meta data values do not depend on the nucleotidesequence strand value.Application specific implementations should inherit from this class tooverride and add to these methods.Bio::Seq::Meta::Array allows for more complex meta values (scalarsor objects) to be used.
Character based meta data is read and set by method meta() and itsvariants. These are the suffixes and prefixes used in the variants:

[named_] [sub] meta [_text]

_text

Suffix _text guaranties that output is a string. Note that it doesnot limit the input. In this implementation, the output is always text, so these methodsare redundant.

sub

Prefix sub, like in subseq(), means that the method applies to subregion of the sequence range and takes start and end as arguments.Unlike subseq(), these methods are able to set values. If the rangeis not defined, it defaults to the complete sequence.

named

Prefix named_ in method names allows the used to attach multiplemeta strings to one sequence by explicitly naming them. The name isalways the first argument to the method. The "unnamed" methods use theclass wide default name for the meta data and are thus special cases"named" methods. Note that internally names are keys in a hash and any misspelling of aname will silently store the data under a wrong name. The used names(keys) can be retrieved using method meta_names(). See meta_names.

Title : meta Usage : $meta_values = $obj->meta($values_string); Function:
Get and set method for the meta data starting from residue
position one. Since it is dependent on the length of the
sequence, it needs to be manipulated after the sequence.
The length of the returned value always matches the length
of the sequence, if force_flush() is set. See force_flush.
Returns : meta data in a string
Args : new value, string, optional

Title : named_meta() Usage : $meta_values = $obj->named_meta($name, $values_arrayref); Function: A more general version of meta(). Each meta data set needs to be named. See also meta_names. Returns : a string Args : scalar, name of the meta data set new value, optional

Title : _test_gap_positions Usage : $meta_values = $obj->_test_gap_positions($name); Function: Internal test for correct position of gap characters. Gap being only '-' this time.
This method is called from named_meta() when setting meta
data but only if verbose is positive as this can be an
expensive process on very long sequences. Set verbose(1) to
see warnings when gaps do not align in sequence and meta
data and turn them into errors by setting verbose(2).
Returns : true on success, prints warnings
Args : none

Title : named_meta_text() Usage : $meta_values = $obj->named_meta_text($name, $values_arrayref); Function: Variant of named_meta() guarantied to return a textual representation of the named meta data. For details, see meta. Returns : a string Args : scalar, name of the meta data set new value, optional

Title : submeta Usage : $subset_of_meta_values = $obj->submeta(10, 20, $value_string); $subset_of_meta_values = $obj->submeta(10, undef, $value_string); Function:
Get and set method for meta data for subsequences.
Numbering starts from 1 and the number is inclusive, ie 1-2
are the first two residue of the sequence. Start cannot be
larger than end but can be equal.
If the second argument is missing the returned values
should extend to the end of the sequence.
The return value may be a string or an array reference,
depending on the implementation. If in doubt, use
submeta_text() which is a variant guarantied to return a
string. See submeta_text.
Returns : A reference to an array or a string
Args : integer, start position
integer, end position, optional when a third argument present
new value, optional

Title : named_submeta Usage : $subset_of_meta_values = $obj->named_submeta($name, 10, 20, $value_string); $subset_of_meta_values = $obj->named_submeta($name, 10); Function: Variant of submeta() guarantied to return a textual representation of meta data. For details, see meta. Returns : A reference to an array or a string Args : scalar, name of the meta data set integer, start position integer, end position, optional when a third argument present new value, optional

Title : meta_names Usage : @meta_names = $obj->meta_names() Function: Retrieves an array of meta data set names. The default (unnamed) set name is guarantied to be the first name. Returns : an array of names Args : none

Title : is_flush Usage : $is_flush = $obj->is_flush() or $is_flush = $obj->is_flush($my_meta_name) Function: Boolean to tell if all meta values are in flush with the sequence length. Returns true if force_flush() is set Set verbosity to a positive value to see failed meta sets Returns : boolean 1 or 0 Args : optional name of the meta set

Title : revcom Usage : $newseq = $seq->revcom(); Function: Produces a new Bio::Seq::MetaI implementing object where the order of residues and their meta information is reversed. Returns : A new (fresh) Bio::Seq::Meta object Args : none Throws : if the object returns false on is_flush()

Title : trunc Usage : $subseq = $seq->trunc(10,100); Function: Provides a truncation of a sequence together with meta data Returns : a fresh Bio::Seq::Meta implementing object Args : Two integers denoting first and last residue of the sub-sequence.

This Bio::Seq::MetaI implementation inherits from Bio::LocatableSeq, whichitself inherits from Bio::PrimarySeq. It is not a Bio::SeqI, so bless-ingobjects of this class into a Bio::SeqI or vice versa and will not work asexpected (see bug 2262). This may be addressed in a future refactor ofBio::LocatableSeq.

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